mpi_util.py

from collections import defaultdict
from mpi4py import MPI
import os, numpy as np
import platform
import tensorflow as tf

def sync_from_root(sess, variables, comm=None):
    """
    Send the root node's parameters to every worker.
    Arguments:
      sess: the TensorFlow session.
      variables: all parameter variables including optimizer's
    """
    if comm is None: comm = MPI.COMM_WORLD
    rank = comm.Get_rank()
    for var in variables:
        if rank == 0:
            comm.bcast(sess.run(var))
        else:
            import tensorflow as tf
            sess.run(tf.assign(var, comm.bcast(None)))

# def gpu_count():
#     """
#     Count the GPUs on this machine.
#     """
#     if shutil.which('nvidia-smi') is None:
#         return 0
#     output = subprocess.check_output(['nvidia-smi', '--query-gpu=gpu_name', '--format=csv'])
#     return max(0, len(output.split(b'\n')) - 2)
#
# def setup_mpi_gpus():
#     """
#     Set CUDA_VISIBLE_DEVICES using MPI.
#     """
#     num_gpus = gpu_count()
#     if num_gpus == 0:
#         return
#     local_rank, _ = get_local_rank_size(MPI.COMM_WORLD)
#     os.environ['CUDA_VISIBLE_DEVICES'] = str(local_rank % num_gpus)

def guess_available_gpus(n_gpus=None):
    if n_gpus is not None:
        return list(range(n_gpus))
    if 'CUDA_VISIBLE_DEVICES' in os.environ:
        cuda_visible_divices = os.environ['CUDA_VISIBLE_DEVICES']
        cuda_visible_divices = cuda_visible_divices.split(',')
        return [int(n) for n in cuda_visible_divices]
    if 'RCALL_NUM_GPU' in os.environ:
        n_gpus = int(os.environ['RCALL_NUM_GPU'])
        return list(range(n_gpus))
    nvidia_dir = '/proc/driver/nvidia/gpus/'
    if os.path.exists(nvidia_dir):
        n_gpus = len(os.listdir(nvidia_dir))
        return list(range(n_gpus))
    raise Exception("Couldn't guess the available gpus on this machine")


def setup_mpi_gpus():
    """
    Set CUDA_VISIBLE_DEVICES using MPI.
    """
    available_gpus = guess_available_gpus()

    node_id = platform.node()
    nodes_ordered_by_rank = MPI.COMM_WORLD.allgather(node_id)
    processes_outranked_on_this_node = [n for n in nodes_ordered_by_rank[:MPI.COMM_WORLD.Get_rank()] if n == node_id]
    local_rank = len(processes_outranked_on_this_node)

    os.environ['CUDA_VISIBLE_DEVICES'] = str(available_gpus[local_rank])
    # os.environ['CUDA_VISIBLE_DEVICES'] = ""   # using cpu instead of gpu



def get_local_rank_size(comm):
    """
    Returns the rank of each process on its machine
    The processes on a given machine will be assigned ranks
        0, 1, 2, ..., N-1,
    where N is the number of processes on this machine.

    Useful if you want to assign one gpu per machine
    """
    this_node = platform.node()
    ranks_nodes = comm.allgather((comm.Get_rank(), this_node))
    node2rankssofar = defaultdict(int)
    local_rank = None
    for (rank, node) in ranks_nodes:
        if rank == comm.Get_rank():
            local_rank = node2rankssofar[node]
        node2rankssofar[node] += 1
    assert local_rank is not None
    return local_rank, node2rankssofar[this_node]

def share_file(comm, path):
    """
    Copies the file from rank 0 to all other ranks
    Puts it in the same place on all machines
    """
    localrank, _ = get_local_rank_size(comm)
    if comm.Get_rank() == 0:
        with open(path, 'rb') as fh:
            data = fh.read()
        comm.bcast(data)
    else:
        data = comm.bcast(None)
        if localrank == 0:
            os.makedirs(os.path.dirname(path), exist_ok=True)
            with open(path, 'wb') as fh:
                fh.write(data)
    comm.Barrier()

def dict_gather_mean(comm, d):
    alldicts = comm.allgather(d)
    size = comm.Get_size()
    k2li = defaultdict(list)
    for d in alldicts:
        for (k,v) in d.items():
            k2li[k].append(v)
    k2mean = {}
    for (k,li) in k2li.items():
        k2mean[k] = np.mean(li, axis=0) if len(li) == size else np.nan
    return k2mean

class MpiAdamOptimizer(tf.train.AdamOptimizer):
    """Adam optimizer that averages gradients across mpi processes."""
    def __init__(self, comm, **kwargs):
        self.comm = comm
        tf.train.AdamOptimizer.__init__(self, **kwargs)
    def compute_gradients(self, loss, var_list, **kwargs):
        grads_and_vars = tf.train.AdamOptimizer.compute_gradients(self, loss, var_list, **kwargs)
        grads_and_vars = [(g, v) for g, v in grads_and_vars if g is not None]
        flat_grad = tf.concat([tf.reshape(g, (-1,)) for g, v in grads_and_vars], axis=0)
        shapes = [v.shape.as_list() for g, v in grads_and_vars]
        sizes = [int(np.prod(s)) for s in shapes]

        num_tasks = self.comm.Get_size()
        buf = np.zeros(sum(sizes), np.float32)

        def _collect_grads(flat_grad):
            self.comm.Allreduce(flat_grad, buf, op=MPI.SUM)
            np.divide(buf, float(num_tasks), out=buf)
            return buf

        avg_flat_grad = tf.py_func(_collect_grads, [flat_grad], tf.float32)
        avg_flat_grad.set_shape(flat_grad.shape)
        avg_grads = tf.split(avg_flat_grad, sizes, axis=0)
        avg_grads_and_vars = [(tf.reshape(g, v.shape), v)
                    for g, (_, v) in zip(avg_grads, grads_and_vars)]

        return avg_grads_and_vars


def mpi_mean(x, axis=0, comm=None, keepdims=False):
    x = np.asarray(x)
    assert x.ndim > 0
    if comm is None: comm = MPI.COMM_WORLD
    xsum = x.sum(axis=axis, keepdims=keepdims)
    n = xsum.size
    localsum = np.zeros(n+1, x.dtype)
    localsum[:n] = xsum.ravel()
    localsum[n] = x.shape[axis]
    globalsum = np.zeros_like(localsum)
    comm.Allreduce(localsum, globalsum, op=MPI.SUM)
    return globalsum[:n].reshape(xsum.shape) / globalsum[n], globalsum[n]

def mpi_moments(x, axis=0, comm=None, keepdims=False):
    x = np.asarray(x)
    assert x.ndim > 0
    mean, count = mpi_mean(x, axis=axis, comm=comm, keepdims=True)
    sqdiffs = np.square(x - mean)
    meansqdiff, count1 = mpi_mean(sqdiffs, axis=axis, comm=comm, keepdims=True)
    assert count1 == count
    std = np.sqrt(meansqdiff)
    if not keepdims:
        newshape = mean.shape[:axis] + mean.shape[axis+1:]
        mean = mean.reshape(newshape)
        std = std.reshape(newshape)
    return mean, std, count

class RunningMeanStd(object):
    # https://en.wikipedia.org/wiki/Algorithms_for_calculating_variance#Parallel_algorithm
    def __init__(self, epsilon=1e-4, shape=(), comm=None, use_mpi=True):
        self.mean = np.zeros(shape, 'float64')
        self.use_mpi = use_mpi
        self.var = np.ones(shape, 'float64')
        self.count = epsilon
        if comm is None:
            from mpi4py import MPI
            comm = MPI.COMM_WORLD
        self.comm = comm


    def update(self, x):
        if self.use_mpi:
            batch_mean, batch_std, batch_count = mpi_moments(x, axis=0, comm=self.comm)
        else:
            batch_mean, batch_std, batch_count = np.mean(x, axis=0), np.std(x, axis=0), x.shape[0]
        batch_var = np.square(batch_std)
        self.update_from_moments(batch_mean, batch_var, batch_count)

    def update_from_moments(self, batch_mean, batch_var, batch_count):
        delta = batch_mean - self.mean
        tot_count = self.count + batch_count

        new_mean = self.mean + delta * batch_count / tot_count
        m_a = self.var * (self.count)
        m_b = batch_var * (batch_count)
        M2 = m_a + m_b + np.square(delta) * self.count * batch_count / (self.count + batch_count)
        new_var = M2 / (self.count + batch_count)

        new_count = batch_count + self.count

        self.mean = new_mean
        self.var = new_var
        self.count = new_count